Minimum vis for fish analysis = 2-m
Kelp depths = 5 -m Fish depths = 5, 10 -m Inv depths = 5 -m
Visibility data for 2015 are fake. DI was bad and set at 1.0 m; other sites set at 3.0 m
## Joining, by = "taxa"
Fish depth = 5, 10
## Joining, by = "taxa"
Kelp depth = 5
## `summarise()` has grouped output by 'year', 'site', 'transect', 'species', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone'. You can override using the `.groups` argument.
## Joining, by = "site"
## Caonopy kelp 5 m only
## Nerocystis at Tatoosh
## Nero and Macro
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site'. You can override using the `.groups` argument.
## Big three
Plot the big 3 species: Macro, Nero, Ptero
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
# INVERTEBRATES
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'species', 'zone', 'area', 'taxa'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone', 'area'. You can override using the `.groups` argument.
Ole will want to clean up the figure
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'area', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
Probably worth dropping into the supplement to show that it was mostly purple urchins. Partly interesting because there is no purple urchin fishery, but there is a red one. I think.
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
facet_grid(rows=“zone”) + #,scales=“free_y”) +
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'area', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
Ugly..no aliby..
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
# COMBINED KELP - URCHIN - SEASTAR PLOTS
## By year and zone summarized across sites
## `summarise()` has grouped output by 'year', 'zone'. You can override using the `.groups` argument.
## Summarized across sites; 5 m and 10 m depths combined
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## Summarized across sites; 5-m depth zone only
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
# Output data for multivariate statistics
Not yet transformed to wide format in order to retain SD & SE info upon saving out. Transform in the Multiariate analysis rmd.
Output data files to use for multivariate ordinations.
Use these files and not raw files. Kelp and invert data have been converted to density to account for different transect lengths etc.
Quick view of what species to include in kelp ordinations. Basically only the big three have any abundance.
## `summarise()` has grouped output by 'species'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'taxa'. You can override using the `.groups` argument.
for multivariate analysis; cut and paste to that file
fish.spp = c(“OPEL”, “HEXA”, “SECA”, “SCMA” ,“SENE”, “SEME”, ‘EMBI’,‘GOBI’)
yoy.spp = c(“SECAyoy”, “SEPIyoy”, “SEMYyoy”, “SEBYTyoy”,“RYOY”)